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A Data Carpentry Workshop

The Jackson Laboratory

Apr 14-15, 2016

9:00 am - 5:00 pm

Instructors: Meeta Mistry, Mary Piper

Helpers: Sue McClatchy, Narayanan Raghupathy, Petr Simecek, Saira Kazmi, Shane Sanders, Sandeep Namburi

General Information

Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data.

We will cover Introduction to the Shell and Cloud Computing, The Shell and Project Setup, Know Your Data and Variant Calling and Workflow Automation. Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.

Who: The workshop is open to researchers at all levels from the Jackson Laboratory and other institutions. We will create a supportive environment in which instructors assist with programming exercises and participants help one another. For this reason, on-site (rather than remote) participation is required.

Where: We'll be in the Staff Conference Room opposite the LCC Auditorium at the Jackson Laboratory, 600 Main Street, Bar Harbor, Maine. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with specific software installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.

Contact: Please mail for more information.

Preliminary Schedule

Thursday, April 14

MorningIntroduction to the Shell and Cloud Computing
09:00 Workshop overview
09:30 Using cloud computing for genomics
10:00 Introduction to Unix: navigating, paths, shortcuts
10:45 Coffee/tea break
11:00 Introduction to Unix: examining files, modifying, writing
12:00 Lunch on your own
Afternoon The Shell and Project Setup
13:00 Introduction to Unix: searching and redirection
13:45 Shell scripts
14:30 Coffee/tea break
14:45 Shell scripts (cont)
15:45 Genomics planning
16:45 Wrap-up

Friday, April 15

Morning Know Your Data
09:00 Introduction to the workshop dataset
09:15 Examining data on the NCBI SRA database
09:45 QC of NGS data
10:30 Coffee/tea break
10:45 QC of NGS data (cont)
12:00 Lunch on your own
Afternoon Variant Calling and Workflow Automation
13:00 Variant calling workflow (QC, alignment, variant calling)
14:00 Automating the workflow
14:30 Coffee/tea break
14:45 Automating the workflow (cont)
16:45 Wrap-up

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


To participate in a Data Carpentry workshop, you will need working copies of the software named below. Please make sure to install everything before the start of your workshop. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Mac users

  1. Java
  2. Filezilla
  3. Integrative Genomics Viewer (IGV) (You will need to enter your email address; don't worry, they don't send spam.)

Windows users

  1. Putty (Download putty.exe)
  2. Java
  3. Filezilla
  4. Integrative Genomics Viewer (IGV) (You will need to enter your email address; don't worry, they don't send spam.)

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.